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Int. J. Mol. Sci. 2010, 11(10), 3725-3747; doi:10.3390/ijms11103725

Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction

Received: 3 September 2010 / Revised: 10 September 2010 / Accepted: 15 September 2010 / Published: 29 September 2010
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Many cell functions in all living organisms rely on protein-based molecular recognition involving disorder-to-order transitions upon binding by molecular recognition features (MoRFs). A well accepted computational tool for identifying likely protein-protein interactions is sequence alignment. In this paper, we propose the combination of sequence alignment and disorder prediction as a tool to improve the confidence of identifying MoRF-based protein-protein interactions. The method of reverse sequence alignment is also rationalized here as a novel approach for finding additional interaction regions, leading to the concept of a retro-MoRF, which has the reversed sequence of an identified MoRF. The set of retro-MoRF binding partners likely overlap the partner-sets of the originally identified MoRFs. The high abundance of MoRF-containing intrinsically disordered proteins in nature suggests the possibility that the number of retro-MoRFs could likewise be very high. This hypothesis provides new grounds for exploring the mysteries of protein-protein interaction networks at the genome level.
Keywords: reverse; retro; invert; alignment; intrinsic disorder; PONDR-RIBS reverse; retro; invert; alignment; intrinsic disorder; PONDR-RIBS
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Xue, B.; Dunker, A.K.; Uversky, V.N. Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction. Int. J. Mol. Sci. 2010, 11, 3725-3747.

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